After I broke through the Titan Gates the #3 trainer option stopped working, which is a shame because that is when you want it most.

the trainer still works in later missions. Please note the following addition to the instructions:

In some cases, MAX GOONS and UPGRADE POINTS do not seem to update. For instance, If you have spent all your Upgrade Points, OR certain docking bases do not allow you to transfer Goons to Rex. If this is the case, follow these instructions (ONLY FOR GOONS AND UPGRADE POINTS).

1) Press ESC to open up the OPTIONS menu2) Select SAVE GAME and name it TEST3) press the option key(s) (this is only for GOONS or UPGRADE POINTS)4) select SAVE GAME and overwrite TEST5) select LOAD GAME and load TEST6) you should see that you have increased GOONS and/or UPGRADE POINTS7) this is only necessary for GOONS and UPGRADE POINTS, so don't use this for other options!

Would it be possible for you guys to change the number of upgrade points given per activation of the upgrade points option? 99 is a massively huge amount, equivalent to gaining 33 levels. I'd like to get enough to remove some of the leveling grind without completely obsoleting the game's leveling mechanic.

I think 10-20 would be preferable, and if you need more, you can just add them. Maybe values like this can be made configurable from a file, like the hotkeys are?

The trainer works fine for me throughout the chapters. What i do for goons to update right away is use the option...bribe gate...exit station and voila..max goons..right now i am clearing the whole system 1 planet at a time of the infection levels and the trainer still works fine. when ever i liberate a new system i head over to UTA station..dock...press option 1 and 2...select large base...and both resources and goons are at max. Mine's steam version and i'm using 64 bit win 7.